EMDB-19137: Composite structure of the Dictyostelium discoideum nuclear pore ...

Basic information

Entry

Database: EMDB / ID: EMD-19137

• Title: Composite structure of the Dictyostelium discoideum nuclear pore complex in cells
• Map data: Composite map of the Dictyostelium discoideum NPC

Sample

• Complex: Nuclear pore complex

• Keywords: nuclear pore complex / NUCLEAR PROTEIN

Function / homology

Function:

protein-heme linkage / COPII-mediated vesicle transport / Amino acids regulate mTORC1 / protein kinase 5 complex / nuclear pore transmembrane ring / bacteriocin transport / mRNA cleavage factor complex / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore inner ring / toxin transmembrane transporter activity / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / cytochrome complex assembly / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / NLS-bearing protein import into nucleus / structural constituent of nuclear pore / nuclear localization sequence binding / cyclin-dependent protein serine/threonine kinase activator activity / mRNA 3'-end processing / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / termination of RNA polymerase II transcription / RNA polymerase II complex binding / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / mRNA transport / endoplasmic reticulum to Golgi vesicle-mediated transport / nuclear pore / mRNA export from nucleus / ribosomal small subunit export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / phospholipid binding / protein import into nucleus / spindle pole / protein transport / microtubule binding / nuclear membrane / oxidoreductase activity / lysosomal membrane / mRNA binding / heme binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / RNA binding / metal ion binding / membrane / plasma membrane / cytoplasm

Domain/homology:

: / Nuclear pore membrane glycoprotein 210-like / : / : / : / : / : / NUP210 Ig-like domain 15 / NUP210 Ig-like domain 7 / NUP210 Ig-like domain 3 / NUP210 Ig-like domain 1 / NUP210 Ig-like domain 2 / CcmE/CycJ protein / CcmE-like superfamily / Aladin / CcmE domain / Tol-Pal system, TolA / Protein PCF11-like / Cyclin-dependent kinase 5 activator / Nucleoporin Nup88 / Nuclear pore component / Nucleoporin NUP88/NUP82 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup155-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / Prismane-like superfamily / Bacterial Ig-like domain, group 2 / Serralysin-like metalloprotease, C-terminal / : / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / G-protein beta WD-40 repeat / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold

Component:

RanBP2-type zinc finger / Protein SEC13 homolog / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin 155 / WD40-like domain-containing protein / Uncharacterized protein / Nucleoporin 210 / Nucleoporin 133 / Nuclear pore complex protein / Nuclear pore complex protein nup85 / Uncharacterized protein / Uncharacterized protein / Nuclear pore complex protein nup43 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Nuclear pore complex protein nup54 / Uncharacterized protein / ELYS-like domain-containing protein / Nuclear pore protein / WD40 repeat-containing protein / Nuclear pore protein / Uncharacterized protein

• Biological species: Dictyostelium discoideum AX2 (eukaryote)
• Method: subtomogram averaging / cryo EM / Resolution: 30.0 Å
• Authors: Hoffmann PC / Kim H / Obarska-Kosinska A / Kreysing J / Andino-Frydman E / Cruz-Leon S / Cernikova L / Kosinski J / Turonova B / Hummer G / Beck M

Funding support

Germany, European Union, 2 items

Organization	Grant number	Country
Max Planck Society		Germany
European Molecular Biology Organization (EMBO)	ALTF 33-2021	European Union

• Citation: Journal: Mol Cell / Year: 2025; Title: Nuclear pore permeability and fluid flow are modulated by its dilation state.; Authors: Patrick C Hoffmann / Hyuntae Kim / Agnieszka Obarska-Kosinska / Jan Philipp Kreysing / Eli Andino-Frydman / Sergio Cruz-León / Erica Margiotta / Lenka Cernikova / Jan Kosinski / Beata Turoňová / Gerhard Hummer / Martin Beck / ; Abstract: Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in osmolarity, to assess which role nuclear pore complexes (NPCs) play in achieving nuclear volume adaptation and relieving mechanical stress. We capitalize on the unique properties of D. discoideum to quantify fluid flow across NPCs. D. discoideum has an elaborate NPC structure in situ. Its dilation state affects NPC permeability for nucleocytosolic flow. Based on mathematical concepts adapted from hydrodynamics, we conceptualize this phenomenon as porous flow across NPCs, which is distinct from canonically characterized modes of nucleocytoplasmic transport because of its dependence on pressure. Viral NPC blockage decreased nucleocytosolic flow. Our results may be relevant for any biological conditions that entail rapid nuclear size adaptation, including metastasizing cancer cells, migrating cells, or differentiating tissues.

History

Deposition	Dec 14, 2023	-
Header (metadata) release	Dec 25, 2024	-
Map release	Dec 25, 2024	-
Update	Feb 19, 2025	-
Current status	Feb 19, 2025	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_19137.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Composite map of the Dictyostelium discoideum NPC
• Voxel size: X=Y=Z: 8.704 Å

Density

Contour Level	By AUTHOR: 1.0
Minimum - Maximum	-7.92542 - 11.922959000000001
Average (Standard dev.)	0.07980484 (±0.60606706)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin -28 -28 -28 Dimensions 240 240 240 Spacing 240 240 240
Cell	A=B=C: 2088.9602 Å α=β=γ: 90.0 °

Supplemental data

Additional map: Symmetrized map of the whole Dictyostelium discoideum NPC

• File: emd_19137_additional_1.map
• Annotation: Symmetrized map of the whole Dictyostelium discoideum NPC

Sample components

Entire : Nuclear pore complex

• Entire: Name: Nuclear pore complex

Components

• Complex: Nuclear pore complex

Supramolecule #1: Nuclear pore complex

• Supramolecule: Name: Nuclear pore complex / type: complex / ID: 1 / Parent: 0
• Source (natural): Organism: Dictyostelium discoideum AX2 (eukaryote)

Experimental details

Structure determination

• Method: cryo EM
• Processing: subtomogram averaging
• Aggregation state: cell

Sample preparation

• Buffer: pH: 7.2
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.3 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Final reconstruction: Applied symmetry - Point group: C₈ (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Number subtomograms used: 4921
• Extraction: Number tomograms: 310 / Number images used: 5960
• Final angle assignment: Type: NOT APPLICABLE